Update

author: Richèl J.C. Bilderbeek date: 2021-07-15 autosize: true

https://github.com/richelbilderbeek/igp_presentation_20210715

Setup

When you are lucky

https://en.wikipedia.org/wiki/File:Eye_disease_simulation,_age-related_macular_degeneration.jpg

Age (years) Incidence
50-60 0.4%
60-70 0.7%
70-80 2.3%
80+ 12%

The first GWAS

https://en.wikipedia.org/wiki/File:Eye_disease_simulation,_age-related_macular_degeneration.jpg

Eagle, R. C. (2006). doi:10.1016/s0084-392x(08)70396-4

https://en.wikipedia.org/wiki/Factor_H#/media/File:2g7i.jpg

Today’s GWAS

Today’s GWAS

Igl et al., 2010

38 citations

Höglund et al., 2019

Kierczak et al., unpublished

Introduction

Quantitive trait associations, e.g. protein levels, are important.

Works well when:

Research question

Can we find novel associations using machine learning?

Novel == un(der)detected using existing methods

GCAE

Problem

PCA is useful

Lao, Oscar, et al. “Correlation between genetic and geographic structure in Europe.” Current Biology 18.16 (2008): 1241-1248.

Lao et al., 2008 figure 1

Potential to do better than PCA

Ausmees, Kristiina and Nettelblad, Carl. “A deep learning framework for characterization of genotype data.” bioRxiv (2020)

Ausmees and Nettelblad, 2020 figure 3a

Do better than PCA using GCAE

Ausmees, Kristiina and Nettelblad, Carl. “A deep learning framework for characterization of genotype data.” bioRxiv (2020)

Ausmees and Nettelblad, 2020 figure 3b

GCAE

Character Full What
G Genomic Works on genomic data
C Convolutional Works on processed data
A Auto Learns by itself
E Encoder to efficiently encode the data

Type of analysis

Research question

Can we find novel associations using GCAE?

Novel == un(der)detected using existing methods

State of GCAE now

Finding novel associations

Proof of concept:

library(plinkr)
set.seed(314)
mafs <- 0.49
n_individuals <- 1000

Random phenotype

A phenotype that is completely unrelated to the SNPs investigated

https://upload.wikimedia.org/wikipedia/commons/6/6c/Hans_am_Tretbrett.jpg

Random phenotype

class: small-code

snvs <- create_snvs(
  n_individuals = 4
)
calc_random_phenotype <- function(snvs) {
  stats::runif(nrow(snvs))
}
snvs$random <- calc_random_phenotype(snvs)
knitr::kable(snvs)
snv_1a snv_1b random
A A 0.0988320
A C 0.2714778
C A 0.7665282
C C 0.2246424

Random trait

class: small-code

random_trait <- create_custom_trait(
  phenotype = "random",
  mafs = 0.49,
  n_snps = 1,
  calc_phenotype_function =
    calc_random_phenotype
)
random_data <- create_demo_assoc_qt_params(
  traits = random_trait,
  n_individuals = n_individuals
)
knitr::kable(
  cbind(
    random_data$ped_table[, -seq(1, 6)],
    random_data$phe_table[, 3]
  )
)
snv_1a snv_1b random
C C 0.4666161
C C 0.3510843
A A 0.9266955
C A 0.9974184
C C 0.4981833
C C 0.4371469
C C 0.3710171
A A 0.4765347
C A 0.8747569
A A 0.0703521
C A 0.5177573
A C 0.7403552
C A 0.6766470
C C 0.3195054
A C 0.6527457
C C 0.2545512
A A 0.4073478
C A 0.8687714
A C 0.9359008
A C 0.7342456
C C 0.4629348
C A 0.9954340
A C 0.4298082
C A 0.5565240
A C 0.2405035
A A 0.2429802
C A 0.4378420
A C 0.9054450
C C 0.0004699
A C 0.5640251
A C 0.8818015
A C 0.5051586
A C 0.8302418
C C 0.4009614
C C 0.9330289
A C 0.1390164
C C 0.5665199
C C 0.8372669
C C 0.5175253
A C 0.2984122
A C 0.3875989
C C 0.6318162
A C 0.1600651
A A 0.5808374
A C 0.7287619
A A 0.9184051
C A 0.9380222
C C 0.0702222
C A 0.9573446
A C 0.4708177
A A 0.2436554
A A 0.6870006
C C 0.6033164
C A 0.5356131
C A 0.0292049
C A 0.4869139
C C 0.2194685
C C 0.6752314
A C 0.2737835
A C 0.0111437
C A 0.6616764
C A 0.9479069
A C 0.8620828
A A 0.7223205
C A 0.6246416
C A 0.2143780
C A 0.8565959
C A 0.4969844
C C 0.2784219
A C 0.5260534
C C 0.8121509
A A 0.0180577
A A 0.2200433
A A 0.0813889
A A 0.4023108
A A 0.1350695
A C 0.3755708
C C 0.4239408
C A 0.2754110
C C 0.9584926
C C 0.7027859
A A 0.1828515
C C 0.9035468
A A 0.1277749
C C 0.8167092
A A 0.2538690
C A 0.0027642
A A 0.1268870
A A 0.6045920
C A 0.9469801
A C 0.1704597
C A 0.8230466
C A 0.0168202
C C 0.0859954
C C 0.4236687
A C 0.7816329
C C 0.9444947
A A 0.5371656
A C 0.1330566
C C 0.2114321
C C 0.5724692
C C 0.5780750
C A 0.9633829
C C 0.9526718
A C 0.5886201
A A 0.0163122
A C 0.0382191
C A 0.3778935
C C 0.0038855
C A 0.0121057
C C 0.4895431
A C 0.0337622
A A 0.2711655
A A 0.1523292
C C 0.3226183
A A 0.4908241
A A 0.7293634
A C 0.0257039
A C 0.7650239
C A 0.5917298
C A 0.6006035
A C 0.5050879
A C 0.6207248
C A 0.3582780
C A 0.6181159
A A 0.7827187
A C 0.8107463
A C 0.3900908
C C 0.5550675
A A 0.8697689
C A 0.6257760
C C 0.1150237
A A 0.2682994
A C 0.6718922
A A 0.4927311
A A 0.3011806
C C 0.9527706
A A 0.7095233
C C 0.1852366
C C 0.0880095
C C 0.9357250
C A 0.5798597
C A 0.9648490
C A 0.8572698
C A 0.3553385
A A 0.9173626
A A 0.1446935
A A 0.3120757
C C 0.8112037
C C 0.4203017
A C 0.8600740
A A 0.4282796
C A 0.7158796
C A 0.9363899
A A 0.8646936
C A 0.7376986
A A 0.4498195
C C 0.9727773
A C 0.9998425
C A 0.1005272
A C 0.9234042
C A 0.6666076
C C 0.7758992
C C 0.9524245
C C 0.6979056
A A 0.5840827
A C 0.4836001
A A 0.5444697
C C 0.6110389
C C 0.4334467
A A 0.3880146
A A 0.9274434
A C 0.9546580
C A 0.2964629
A A 0.8237353
C A 0.3723806
A A 0.2829903
A C 0.4270406
C A 0.6376593
A A 0.7983570
C C 0.9672294
C A 0.9162136
C A 0.0765617
C A 0.0258274
A C 0.7534460
C A 0.6852524
A C 0.5883287
A A 0.3084476
C C 0.9655612
C A 0.4132219
C A 0.1131252
C A 0.9391504
A C 0.1644022
A A 0.6183585
A A 0.2059833
A A 0.0693161
A C 0.6643047
A A 0.6711986
C A 0.1668075
A C 0.4708659
C C 0.0919447
A C 0.7919454
A A 0.2781073
C C 0.7272416
C C 0.8716855
C A 0.6365015
C A 0.4435521
A C 0.4834481
C C 0.0300629
C A 0.0607565
C A 0.7375413
C C 0.1812268
A C 0.9947233
C C 0.2821435
A A 0.5398953
C A 0.6412068
C C 0.7300088
A A 0.1584773
A A 0.6409074
A C 0.5719852
C C 0.6577698
C A 0.4374673
C C 0.0751168
C A 0.8529090
A A 0.1090336
A C 0.4546626
C C 0.0300427
A A 0.5566143
A A 0.3970274
A C 0.2698140
A C 0.2315345
C A 0.3791137
C C 0.1723093
A C 0.3270362
A A 0.0662876
C A 0.6814550
A C 0.3778047
C A 0.7434023
A A 0.9084648
C C 0.7016574
C C 0.9376146
A A 0.3336255
A C 0.0929231
A C 0.3122960
A A 0.6207482
A A 0.0894140
C A 0.4606120
C C 0.9397063
A C 0.2824683
A A 0.4579554
A A 0.5545835
A C 0.0274181
C A 0.0861547
C C 0.9054060
A C 0.4573563
C A 0.6247406
A A 0.5317663
C C 0.3005938
C C 0.1392729
A A 0.2387616
A C 0.1973084
C C 0.6949484
C C 0.5096948
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C A 0.1956676
A C 0.6238853
C A 0.4144428
A C 0.3102670
A C 0.8887328
A C 0.0651954
C A 0.8564127
C C 0.8273041
A A 0.1106101
C A 0.5602648
A A 0.5980109
C C 0.8423409
C C 0.7017333
A A 0.3589375
C C 0.4320411
A A 0.3000680
A A 0.2733039
C A 0.9491902
C C 0.6232438
C A 0.5312069
A C 0.8239511
A C 0.6032270
A A 0.9730198
C C 0.2214207
A C 0.7614851
A A 0.3774368
C A 0.9415224
C C 0.8791712
A A 0.9317173
A A 0.2708685
A C 0.8860205
A C 0.5942857
A A 0.5006507
A C 0.7532699
A C 0.5723658
C A 0.6797457
C C 0.8078294
C C 0.9364945
A A 0.7718503
C A 0.4540436
A C 0.5019872
A C 0.4921837
C C 0.6803712
A A 0.6168179
A C 0.1636093
C A 0.1297464
A C 0.0467316
C A 0.7535574
A C 0.2825315
C C 0.5807508
A A 0.6842838
A C 0.3901077
A C 0.2145733
C C 0.5894208
C A 0.0924488
A A 0.5320341
A C 0.0799992
C C 0.5880456
C A 0.4731335
C C 0.1679480
C A 0.7268089
C C 0.9582479
A C 0.4659862
A C 0.3902719
A C 0.5835994
C A 0.9905484
C C 0.3358580
C A 0.6327363
C C 0.9960790
A C 0.6282579
A A 0.5723205
C A 0.0441136
A A 0.5927434
C A 0.1058055
C A 0.6372760
C A 0.1617871
A A 0.7651678
A C 0.2782309
A A 0.2005444
C A 0.2166562
A C 0.1304861
A A 0.4531552
A C 0.6676283
C A 0.9269115
A A 0.4658814
C A 0.5433713
A A 0.7827837
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A C 0.8840102
C C 0.6096605
C C 0.2648941
C C 0.4075191
C C 0.8307778
C C 0.7968948
C C 0.1388298
A A 0.9912732
C A 0.7109792
A A 0.4586971
C C 0.9792808
C A 0.6055506
A A 0.7651727
A A 0.3540049
A A 0.8544064
A A 0.3275437
A A 0.6680774
A A 0.6450859
A C 0.1256085
C A 0.9879515
C A 0.3822403
A C 0.5895235
A C 0.6756132
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A C 0.2013024
C C 0.4566241
C C 0.6708180
C A 0.3597837
A C 0.5049601
A A 0.5807733
A A 0.2570299
C A 0.0312179
C C 0.4180220
A A 0.6158686
A C 0.3979164
C A 0.2347665
A A 0.7863461
C A 0.7588834
C A 0.6698301
C C 0.0199496
A A 0.3171380
C C 0.7460284
C A 0.8814165
C A 0.9444794
C A 0.6895219
A A 0.8037568
A C 0.6065219
A A 0.5186909
A A 0.3691207
C A 0.7582214
C C 0.4658594
C C 0.0109562
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C C 0.3225180
A C 0.3721057
A A 0.8311548
A C 0.7403355
A A 0.2121572
A A 0.9137420
C C 0.5756018
A C 0.6160652
C C 0.6574057
C C 0.4914116
C A 0.2492873
C C 0.1104924
A A 0.5445646
C C 0.4836012
A A 0.7877096
C A 0.6815864
A C 0.5830562
A C 0.2364739
C C 0.8665226
C C 0.1136608
A C 0.8163246
C C 0.0798466
C C 0.5734623
C C 0.1143040
A C 0.5521747
C C 0.7928454
A C 0.3337094
C C 0.4243316
C A 0.5178803
A A 0.2550578
C A 0.9746749
A C 0.4399638
C C 0.8821483
A C 0.5132134
C A 0.8709597
A A 0.7688647
C C 0.9730690
A A 0.6724718
A A 0.0793417
A A 0.0568489
C C 0.5389315
C A 0.7198852
A C 0.8596539
C A 0.3299948
C A 0.1809232
C A 0.1541132
A C 0.4853563
C A 0.0763109
A A 0.6944921
A C 0.0913871
A C 0.2556522
C A 0.5825426
C C 0.3350374
A C 0.0817167
A C 0.0326506
A C 0.3916646
A A 0.3329409
A A 0.4059414
A A 0.3480986
A A 0.5644677
A C 0.0820233
C C 0.7641447
C C 0.9782927
A C 0.6282667
C A 0.2604343
A A 0.1055512
C C 0.3294907
A A 0.2784329
A C 0.3182845
A A 0.4178078
A A 0.3412568
A C 0.4434163
C A 0.0523547
C C 0.8839304
A C 0.0279326
C C 0.9090986
C C 0.7269895
A C 0.5814303
A A 0.5198086
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A C 0.8720374
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A C 0.6709002
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C C 0.4284022
C C 0.9457046
A C 0.1184846
C C 0.3919949
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C A 0.5446679
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A C 0.2926608
C C 0.9292295
A A 0.5777770
A C 0.0705725
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C C 0.3770013
C C 0.5488359
C A 0.4962836
C A 0.9188033
C A 0.7398807
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C C 0.0891043
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C A 0.5419761
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C A 0.1115674
A C 0.7893450
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A A 0.3102403
C C 0.4486753
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C A 0.3031048
C C 0.5282730
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A C 0.7473248
A C 0.2220238
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C C 0.2782372
C C 0.7389831
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A C 0.2916470
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A A 0.5165332
A A 0.0532552
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C A 0.6980632
C A 0.7042008
C A 0.0180456
C A 0.4890411
C C 0.3586478
C C 0.7681677
C A 0.7762700
C C 0.9220175
A C 0.2605463
A A 0.6112005
A C 0.5194468
C A 0.9498760
A C 0.9781126
A C 0.4260136
A A 0.9400258
C A 0.0753193
A C 0.6347329
A A 0.1111704
A C 0.9178106
A A 0.0084370
A C 0.7032672
A C 0.6268811
A C 0.7864589
C C 0.2446179
A C 0.8149701
A A 0.5030566
C C 0.6979812
A C 0.7457462
C A 0.4749425
A A 0.9244362
C C 0.8343865
A C 0.4354053
A C 0.4199613
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C A 0.4967197
C A 0.4116587
C A 0.2135292
C C 0.7614026
A C 0.9789993
A A 0.6061888
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C A 0.8388331
C C 0.7525550
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C C 0.8017420
C A 0.9695920
C C 0.1236853
A A 0.9120288
A A 0.3156028
A A 0.8655264
C C 0.1944189
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C A 0.7681128
C A 0.1944977
A A 0.8549429
C C 0.0231320
A A 0.3286483
A A 0.6407425
A A 0.8321432
A A 0.6892191
A C 0.5677826
C C 0.3923747
C C 0.1019067
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A C 0.1782497
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A C 0.6104559
C C 0.5210718
C C 0.4700686
C A 0.3273444
C A 0.3160120
C A 0.1786410
C A 0.0658570
C C 0.4093793
A A 0.6046722
A C 0.0858282
C A 0.3388073
A C 0.3834126
C A 0.0116835
A A 0.0112445
C A 0.4121569
A C 0.9247135
A C 0.1454897
A A 0.2454147
A A 0.9511524
C A 0.6405375
C A 0.2474059
C A 0.3827176
A C 0.3558224
A C 0.0385165
C C 0.7631317
A A 0.0603459
A C 0.7562703
C C 0.8110166
C C 0.1020797
A C 0.4861379
A A 0.8026842
A C 0.1012761
A A 0.9824437
A C 0.5367259
A A 0.3918665
C C 0.4767991
C C 0.4829490
A A 0.9996209
C C 0.3729697
A C 0.1410470
A A 0.2062874
C C 0.9618192
C C 0.0906319
C A 0.5334823
A A 0.5464305
C C 0.9904428
A A 0.9420824
A C 0.4738046
C A 0.1177171
C A 0.2939928
A A 0.7020855
A A 0.1635664
A A 0.1304048
A C 0.3013606
A A 0.3560951
A A 0.9182480
C C 0.9419227
C C 0.6407294
C A 0.9975696
C A 0.1684956
C A 0.1338170
A C 0.7395642
A A 0.7951193
A A 0.3942684
C C 0.3185834
A A 0.1769174
A C 0.8473011
A A 0.7013506
A A 0.7514620
A C 0.1314984
A C 0.7492562
C A 0.6941915
A A 0.0894323
C A 0.2023432
A C 0.9676830
A C 0.8427891
A A 0.8668877
C C 0.4233567
A A 0.5595452
C A 0.4989349
A C 0.8534839
A C 0.6549371
A A 0.6801301
C A 0.2197171
A C 0.0720694
A C 0.6260967
A A 0.4657452
C A 0.5047930
A C 0.6344040
C C 0.0371545
C A 0.6377103
A A 0.1216814
C A 0.0817386
C A 0.7859042
C C 0.2358361
A A 0.7904143
A A 0.4276631
A C 0.9634062
A C 0.4589111
A C 0.7922427
A C 0.2395715
A A 0.2957950
A C 0.5664626
A C 0.3977834
A C 0.7897962
C A 0.7960711
C A 0.5024974
A C 0.1899999
C A 0.1612482
A A 0.1777423
A A 0.9264901
A A 0.3763493
C A 0.5371158
A A 0.0746483
C C 0.8766525
A A 0.1646734
C A 0.5599592
A A 0.8225924
C C 0.6737581
A A 0.1107575
C A 0.9393545
C C 0.6835719
C A 0.5665965
A A 0.9557607
C C 0.5076551
C A 0.6653639
A C 0.0002148
A A 0.0426709
C A 0.5900110
C C 0.5154159
C A 0.2601222
C A 0.4304230
C A 0.1899322
C C 0.7844609
C A 0.6725929
A A 0.4455120
C A 0.6318241
A A 0.1208290
C C 0.6405798
C C 0.0772491
C A 0.0075431
C C 0.1039240
A A 0.0486205
A A 0.4838083
C C 0.7950885
A A 0.5251844
A A 0.8911304
C A 0.8988009
C A 0.5750265
A C 0.2756697
A A 0.8558785
C A 0.1155735
C C 0.5339752
C A 0.2779338
C A 0.9846536
C A 0.4794410
A C 0.2742371
A C 0.7986782
A A 0.8771590
A A 0.3869111
C A 0.6041917
A C 0.7879579
C C 0.8875683
C C 0.1976407
C A 0.9041664
A C 0.8137890
A A 0.1112325
C A 0.4248483
C A 0.6160928
C C 0.6551671
C A 0.4247597
C C 0.2352774
C C 0.8606986
A C 0.2716826
A C 0.1273805
A A 0.2708936
C C 0.0139387
C A 0.9731068
C A 0.3391411
A A 0.8744968
A C 0.6225029
C C 0.6996219
C C 0.8130248
C A 0.5553371
C C 0.5842930
A C 0.4082653
C C 0.2432749
A C 0.3091446
A C 0.3561779
A C 0.0928875
C C 0.8022082
C C 0.1010219
A C 0.8901768
A A 0.8534160
A A 0.3722945
C C 0.5155753
C C 0.5727323
A A 0.0770026
A A 0.0305304
A C 0.6693833
C C 0.6647151
C A 0.8616880
C C 0.7976026
C C 0.2079309
C C 0.8157047
C C 0.7375956
C A 0.0621384
C A 0.7466082
A A 0.4936111
C A 0.9351776
A C 0.5385510
A A 0.0314340
C A 0.9989825
C C 0.7983505
C A 0.0426443
A A 0.6620382
A C 0.8996151
C A 0.0917038
A C 0.2327766
C C 0.2236708
C A 0.5038954
C A 0.6588374
C A 0.2690986
C A 0.4553947
A C 0.5775289
C C 0.1020962
A A 0.4610585
C C 0.7774649
A C 0.9293922
A A 0.6641263
C A 0.6705401
A A 0.4327305
C C 0.6703399
C C 0.8812089
A A 0.7050738
A A 0.7593923
A A 0.7045978
A A 0.5074407
C C 0.2840270
A A 0.4745199
A C 0.6338311
A C 0.9185726
C A 0.4434773
A C 0.8463547
A C 0.5151644
A A 0.1037102
C C 0.3982917
A C 0.8519634
C C 0.9701751
C C 0.4188398
A C 0.1870167
A A 0.4019237
C C 0.8302911
C C 0.7966104
A C 0.9825703
C C 0.2527198
C A 0.6009068
C A 0.1913789
A C 0.3528933
C A 0.2112345
A C 0.9879303
C C 0.0699386
C C 0.0699394
A C 0.0221869
A C 0.2304051
C C 0.8442560
C C 0.4411132
A A 0.5321461
A A 0.8815089
A A 0.6678429
A A 0.9270807
A C 0.6148443
A C 0.9492530
A A 0.7123162
A A 0.7222642
A A 0.3332822
C A 0.7988101
C C 0.0464513
A A 0.9517916
C A 0.0534337
C A 0.2499527
A C 0.7470510
C A 0.8186687
C A 0.4447032
C C 0.7206328
A A 0.8637040
C C 0.6374391
A A 0.9580782
A C 0.8273690
A C 0.9498859
A A 0.4806838
A C 0.1679107
A C 0.8089452
C C 0.2103624
C A 0.7600507
A C 0.7592641
A A 0.5046873
C A 0.8910522
A A 0.4673860
A A 0.7400161
C C 0.0743672
A C 0.5748291
C A 0.7306150
C A 0.6962998
C C 0.2244872
A C 0.1923304
C C 0.4086744
A C 0.2392953
C C 0.3710278
A A 0.1518727
A C 0.5966447
A C 0.6562796
A A 0.0506342
C C 0.3896968
C A 0.1389603
A C 0.7537261
C C 0.6082859
A C 0.6611963
A C 0.6317300
C A 0.1050916
C A 0.8477488
A C 0.1766640
C A 0.9001773
C A 0.0394498
C A 0.5863107
C C 0.7970429
C A 0.8111590
C C 0.0725563
C A 0.6473193
C C 0.7732047
A C 0.4574499
C A 0.1931646
A A 0.5412246
A A 0.1321397
C A 0.7389283
A A 0.3900107
C C 0.9087116
C C 0.2238422
A A 0.7497868
A A 0.4241231
A C 0.9054928
A C 0.9787024
A A 0.0189182
A C 0.7707907
C C 0.3104862
C C 0.9808219
C C 0.5706555
C A 0.3304665
A A 0.7558455
A A 0.5256735
C A 0.4503466
A A 0.4755245
A C 0.4897302
A A 0.9932242
C A 0.8762484
C A 0.5656362
C A 0.3998546
C A 0.2375648
C C 0.8907967
C A 0.8139643
A C 0.1614114

Associations on random data

knitr::kable(assoc_qt(random_data))
CHR SNP BP NMISS BETA SE R2 T P
1 snp_1 1 1000 0.01843 0.01278 0.002079 1.442 0.1496

No association is correctly detected.

Additive phenotype

https://doi.org/10.1016/j.ajhg.2015.01.001

Zhu, Zhihong, et al. “Dominance genetic variation contributes little to the missing heritability for human complex traits.” The American Journal of Human Genetics 96.3 (2015): 377-385. Additive phenotype ======================================================== class: small-code

snvs <- create_snvs(
  n_individuals = 4
)
calc_additive_phenotype <- function(snvs) {
  (rowSums(snvs == "C") / 10.0) +
    runif(nrow(snvs), min = 0.0, max = 0.01)
}
snvs$additive <- calc_additive_phenotype(snvs)
knitr::kable(snvs)
snv_1a snv_1b additive
A A 0.0038967
A C 0.1040717
C A 0.1007025
C C 0.2061279

Additive trait

class: small-code

additive_trait <- create_custom_trait(
  phenotype = "additive",
  mafs = 0.49,
  n_snps = 1,
  calc_phenotype_function =
    calc_additive_phenotype
)
additive_data <- create_demo_assoc_qt_params(
  traits = additive_trait,
  n_individuals = n_individuals
)
knitr::kable(
  cbind(
    additive_data$ped_table[, -seq(1, 6)],
    additive_data$phe_table[, 3]
  )
)
snv_1a snv_1b additive
C C 0.2001345
A A 0.0035830
C A 0.1023847
C A 0.1053521
A A 0.0005797
C A 0.1069706
A C 0.1089242
A A 0.0018606
A A 0.0006008
A C 0.1050057
C A 0.1084381
A C 0.1023191
C C 0.2030954
A A 0.0059369
C C 0.2033870
A C 0.1099877
A C 0.1014320
A A 0.0080159
A A 0.0022211
C A 0.1028064
A A 0.0023147
C C 0.2085766
C C 0.2092915
C A 0.1077363
A C 0.1060595
A C 0.1000014
A C 0.1096937
C C 0.2041953
C C 0.2011429
C C 0.2035675
A A 0.0047397
A A 0.0045488
A A 0.0054612
A C 0.1020763
C C 0.2012229
C C 0.2026017
C A 0.1046448
A C 0.1052374
A A 0.0080201
A C 0.1074549
A C 0.1002790
A A 0.0056149
A A 0.0029349
C C 0.2070543
C A 0.1001834
A A 0.0098399
C A 0.1017337
A A 0.0041087
C C 0.2093328
C A 0.1089980
C C 0.2011987
C A 0.1005397
C C 0.2076037
A A 0.0010833
C C 0.2044853
C A 0.1003411
C C 0.2064810
A C 0.1045995
A A 0.0056039
A C 0.1082579
A A 0.0057842
C A 0.1051864
A C 0.1037307
C C 0.2077717
A C 0.1029206
C A 0.1033148
A C 0.1075623
C C 0.2063942
C C 0.2076909
A A 0.0092659
C A 0.1056850
C A 0.1097527
C C 0.2083913
A C 0.1035066
C C 0.2033116
A C 0.1050027
A A 0.0017325
A A 0.0005382
A A 0.0077776
C A 0.1029726
C C 0.2050786
C A 0.1003037
C C 0.2053894
C C 0.2094487
A C 0.1041370
C C 0.2039290
C C 0.2068436
A C 0.1006486
C C 0.2070922
C C 0.2066137
A C 0.1004581
A A 0.0017768
A A 0.0063865
A A 0.0068809
A A 0.0037155
A A 0.0016965
A C 0.1085090
A A 0.0021160
A C 0.1001600
A A 0.0027507
A A 0.0026556
A A 0.0002404
A C 0.1029901
C A 0.1043545
C A 0.1099595
A A 0.0086970
A C 0.1045438
A C 0.1049376
C C 0.2071166
C C 0.2079192
C C 0.2081927
C C 0.2055672
C A 0.1067905
A A 0.0015151
C C 0.2007278
A A 0.0060519
A A 0.0041687
C C 0.2024370
A C 0.1044643
C A 0.1090913
A A 0.0015422
A C 0.1025600
A A 0.0064843
C A 0.1075814
C C 0.2019401
C A 0.1025182
A A 0.0034234
C C 0.2093051
A C 0.1086873
C C 0.2007415
C A 0.1041916
A A 0.0077269
C A 0.1045826
C A 0.1048819
C C 0.2001348
A A 0.0063951
A A 0.0006930
C C 0.2097524
A A 0.0002169
C A 0.1084613
C A 0.1083236
A A 0.0029324
A A 0.0011612
A A 0.0054296
C C 0.2015380
C A 0.1036786
A C 0.1089022
C A 0.1089866
A C 0.1015136
C C 0.2041375
C C 0.2015008
C C 0.2026065
C C 0.2033848
A C 0.1052731
C C 0.2025727
A A 0.0005389
C C 0.2093132
A A 0.0043518
A A 0.0096246
A A 0.0037314
A C 0.1079498
A C 0.1097988
A A 0.0032608
C C 0.2046164
A C 0.1069920
C A 0.1001034
A C 0.1048619
C C 0.2026475
C C 0.2063604
A C 0.1084121
A C 0.1041226
C C 0.2039830
C A 0.1064859
C C 0.2090100
A C 0.1023748
C C 0.2044626
A C 0.1092510
C A 0.1017601
C A 0.1065368
A C 0.1064021
C C 0.2057010
C A 0.1076512
A C 0.1003910
A A 0.0036809
C C 0.2024031
A C 0.1090589
C A 0.1069486
A C 0.1061878
A C 0.1029161
A A 0.0023220
A C 0.1014354
C A 0.1080553
A C 0.1031640
C C 0.2075213
A A 0.0040311
C C 0.2032586
C A 0.1097486
C A 0.1012034
A A 0.0076690
A C 0.1073132
C C 0.2045700
C A 0.1098273
C C 0.2011183
A A 0.0015650
A A 0.0059164
A C 0.1029541
C C 0.2041919
A C 0.1042958
A A 0.0010377
A C 0.1035567
C C 0.2024033
C A 0.1074836
A C 0.1097111
A A 0.0038766
C C 0.2017587
C A 0.1016002
A A 0.0049921
A A 0.0070670
C A 0.1033418
C C 0.2063053
C C 0.2087062
A A 0.0008121
A C 0.1062835
A C 0.1068736
A A 0.0015615
C A 0.1033098
A C 0.1010805
A C 0.1029935
C A 0.1029169
C A 0.1047229
C A 0.1065302
A A 0.0082923
A C 0.1095570
A A 0.0094658
A A 0.0089069
A C 0.1048502
C C 0.2062819
C A 0.1054871
A C 0.1079688
C A 0.1075643
C C 0.2028836
C A 0.1043019
A A 0.0002519
C A 0.1075941
A C 0.1087524
A A 0.0042368
A C 0.1089094
C C 0.2063222
A C 0.1064506
A A 0.0050273
C C 0.2090311
A A 0.0037761
C A 0.1082944
A C 0.1051513
A C 0.1068148
C A 0.1029368
A C 0.1021110
C C 0.2028452
C A 0.1009362
C C 0.2027872
C A 0.1051931
C C 0.2095383
A A 0.0045381
C C 0.2099808
A C 0.1069918
A A 0.0073257
A A 0.0064326
A C 0.1036158
C A 0.1029028
C A 0.1024084
C A 0.1098565
C A 0.1005166
C C 0.2031574
A C 0.1097027
A A 0.0078638
C C 0.2032503
A C 0.1075915
A C 0.1036569
C A 0.1027754
C C 0.2000502
A C 0.1020861
C C 0.2026240
A C 0.1055614
C C 0.2076808
A C 0.1015924
C C 0.2051292
C A 0.1002043
A A 0.0004281
A C 0.1065349
A A 0.0079634
A C 0.1081532
C C 0.2027335
C A 0.1066254
A C 0.1075581
C A 0.1052134
A A 0.0052006
C A 0.1003758
C C 0.2054060
A C 0.1014441
A C 0.1047099
C C 0.2085333
C A 0.1076920
C C 0.2083775
C C 0.2032598
A A 0.0033421
A C 0.1042887
A A 0.0028927
A A 0.0055347
A C 0.1092204
A C 0.1001152
C C 0.2093101
A C 0.1075800
A A 0.0016423
C C 0.2039244
A A 0.0032759
C A 0.1075292
A A 0.0037327
C C 0.2088403
A A 0.0024771
A C 0.1045607
A A 0.0064402
A A 0.0087025
C A 0.1072772
A C 0.1073439
A C 0.1079637
C A 0.1041916
A A 0.0025665
A C 0.1009521
A A 0.0089158
C C 0.2066248
A C 0.1077897
C C 0.2046282
A A 0.0089321
C A 0.1024962
A C 0.1084776
A C 0.1027256
A C 0.1060330
C A 0.1013844
A C 0.1055542
C C 0.2050387
A C 0.1020484
A A 0.0003270
A A 0.0064196
C C 0.2069516
A C 0.1044548
C A 0.1076580
C C 0.2043757
A A 0.0036577
A A 0.0060534
C A 0.1094668
A C 0.1006972
A C 0.1038206
A C 0.1082395
A A 0.0087275
A C 0.1028011
C A 0.1044975
C C 0.2032320
A C 0.1000925
C A 0.1000832
C C 0.2037938
A A 0.0007316
C A 0.1013913
C C 0.2089102
A A 0.0092961
C C 0.2064432
C A 0.1091472
A A 0.0029493
A C 0.1038467
A C 0.1043683
C C 0.2000977
A A 0.0096264
C A 0.1030810
C C 0.2071391
A A 0.0036449
A A 0.0041078
C A 0.1084572
C A 0.1003942
C A 0.1097737
C A 0.1012496
C A 0.1085659
C C 0.2092190
C A 0.1069667
A A 0.0082523
C A 0.1068874
C C 0.2072094
A C 0.1015693
C C 0.2052441
C C 0.2082710
C A 0.1058486
C C 0.2010231
A A 0.0092764
A A 0.0058992
C C 0.2033106
A A 0.0042265
A A 0.0083598
C A 0.1079429
A C 0.1005901
A A 0.0071879
A A 0.0027791
C A 0.1020563
A A 0.0016369
A C 0.1035759
C C 0.2027799
C A 0.1098044
C C 0.2060675
A C 0.1019345
A A 0.0089523
A C 0.1067570
A A 0.0075206
C A 0.1084945
A C 0.1082591
A C 0.1083380
A A 0.0068559
C A 0.1007404
C A 0.1080892
A A 0.0049616
C A 0.1093175
C A 0.1016522
C C 0.2077733
A A 0.0005095
A C 0.1028709
C C 0.2034431
A A 0.0014703
A A 0.0004128
C A 0.1087299
C C 0.2046786
C A 0.1005526
C C 0.2042106
A A 0.0024032
C C 0.2087338
A C 0.1001473
A A 0.0029913
A A 0.0072218
C C 0.2041333
C C 0.2059208
C A 0.1038899
A C 0.1040284
C C 0.2095852
C A 0.1060037
A C 0.1011649
A A 0.0097105
A A 0.0057150
A C 0.1028203
A C 0.1031190
C A 0.1006120
A A 0.0031889
A C 0.1073314
C A 0.1090091
A C 0.1015117
C C 0.2089782
C A 0.1063983
C C 0.2059702
C A 0.1060347
C A 0.1090694
C C 0.2030218
A A 0.0075704
A A 0.0095580
A C 0.1086542
C A 0.1026623
A C 0.1094137
C C 0.2052773
A C 0.1006339
A C 0.1030232
C C 0.2046393
A A 0.0013274
A A 0.0095300
C C 0.2057215
A C 0.1030079
C A 0.1090685
A A 0.0001077
C C 0.2028376
C A 0.1037775
A A 0.0002552
A C 0.1040291
A A 0.0099021
C C 0.2021005
A C 0.1000609
A C 0.1036054
C C 0.2053793
C C 0.2004941
C C 0.2040068
A A 0.0019378
A C 0.1011605
C C 0.2021554
C A 0.1040450
C C 0.2055633
C A 0.1058654
C C 0.2068447
C C 0.2070774
C C 0.2044591
C A 0.1023905
C C 0.2049679
C A 0.1090468
C C 0.2076719
C A 0.1077369
C C 0.2002493
C A 0.1096146
C A 0.1035319
A A 0.0004373
C A 0.1087651
A A 0.0087918
A C 0.1001747
C A 0.1094938
A C 0.1087396
A A 0.0007139
C A 0.1060227
A C 0.1004070
A C 0.1011735
A A 0.0071202
A A 0.0023324
A C 0.1052538
A A 0.0039247
C A 0.1029682
A A 0.0001661
C A 0.1045111
C C 0.2028671
C A 0.1084758
C A 0.1050526
C C 0.2044098
A A 0.0034096
C A 0.1010419
C A 0.1002349
A C 0.1012938
A A 0.0042111
C A 0.1092317
A A 0.0005314
C A 0.1027641
A A 0.0006976
A A 0.0059262
A A 0.0090875
C A 0.1017007
C C 0.2061476
C A 0.1094093
C A 0.1074382
A A 0.0061305
A C 0.1081789
A A 0.0029955
C C 0.2059311
A C 0.1001573
C C 0.2059439
C C 0.2095260
A A 0.0002275
C A 0.1089683
C A 0.1042173
C A 0.1013811
C A 0.1075982
A A 0.0007373
C C 0.2086883
A A 0.0066158
C C 0.2089862
A C 0.1022184
C C 0.2080956
A A 0.0063738
A C 0.1026643
A C 0.1082529
A C 0.1000397
C A 0.1033214
C C 0.2097367
A A 0.0019888
C A 0.1093363
A A 0.0060884
A C 0.1017966
A C 0.1005280
A C 0.1089720
A C 0.1090451
A C 0.1017959
C C 0.2016410
C C 0.2054955
C C 0.2012397
A A 0.0031768
A A 0.0069890
A C 0.1021115
C A 0.1044951
C A 0.1092024
A C 0.1075797
A C 0.1077012
A C 0.1097675
A A 0.0022042
C C 0.2084285
C C 0.2069840
C A 0.1068630
C C 0.2097429
C A 0.1037399
A A 0.0045708
C A 0.1082478
A C 0.1057078
C C 0.2096548
A C 0.1048772
A A 0.0029792
C C 0.2017846
C C 0.2006963
C C 0.2098875
A A 0.0038926
C A 0.1010932
A A 0.0003468
A C 0.1030456
A A 0.0036705
A C 0.1078713
C A 0.1005561
A C 0.1063571
C C 0.2089823
A A 0.0085762
A A 0.0050809
C A 0.1023808
C A 0.1074656
C C 0.2072080
A C 0.1077854
A C 0.1079360
A C 0.1061646
C A 0.1072907
A C 0.1063067
C A 0.1033325
A A 0.0037981
C C 0.2086743
C A 0.1097386
C C 0.2085420
C A 0.1048677
C C 0.2055260
A A 0.0082194
A A 0.0062467
C A 0.1035184
A A 0.0030221
A C 0.1008503
A C 0.1000136
C A 0.1036397
C A 0.1062002
C A 0.1061710
C A 0.1017129
C A 0.1032231
A A 0.0063761
C C 0.2064750
C C 0.2022226
A C 0.1091733
A A 0.0064618
A A 0.0084215
C C 0.2071592
A C 0.1089278
C A 0.1063172
C A 0.1078012
A C 0.1038597
A C 0.1013259
A A 0.0071703
C C 0.2070604
C C 0.2071973
A A 0.0090835
C A 0.1054635
C A 0.1043283
A A 0.0081247
A C 0.1083681
A A 0.0056144
A C 0.1071056
C C 0.2040757
A A 0.0074696
C A 0.1017408
A C 0.1029973
C C 0.2002477
C A 0.1015532
C A 0.1063173
A A 0.0015141
A A 0.0043867
A A 0.0020748
C A 0.1016015
A C 0.1001028
C C 0.2033488
C C 0.2059610
A C 0.1084401
C C 0.2059321
A C 0.1049264
C A 0.1031694
C A 0.1003591
C A 0.1033975
A C 0.1065793
A A 0.0071433
C A 0.1007311
A A 0.0057025
A C 0.1090507
A C 0.1022610
C A 0.1080890
A C 0.1087481
A A 0.0052728
C C 0.2043440
A A 0.0033352
C C 0.2048579
A C 0.1057698
A A 0.0090046
A C 0.1024363
A A 0.0025662
A A 0.0058716
C C 0.2004678
C A 0.1069020
C C 0.2069458
C A 0.1078559
C A 0.1050637
A C 0.1082012
A A 0.0046341
A A 0.0091965
A A 0.0040570
C C 0.2053070
C A 0.1034255
A C 0.1032237
C C 0.2020856
A C 0.1013295
A C 0.1011642
A A 0.0029731
A A 0.0028415
A A 0.0090742
C C 0.2005457
A C 0.1048641
A A 0.0042378
A C 0.1026630
A A 0.0005094
C C 0.2000952
C A 0.1020843
C C 0.2050337
A A 0.0062792
C C 0.2082651
C C 0.2035859
A A 0.0058338
A C 0.1075437
A A 0.0060577
A C 0.1035764
C A 0.1056779
C A 0.1073068
C C 0.2039563
C C 0.2026859
A A 0.0036335
A C 0.1094857
A C 0.1028160
C A 0.1086489
C A 0.1073270
C C 0.2046995
A C 0.1060796
A A 0.0094262
A A 0.0038777
A A 0.0055042
C A 0.1060838
A A 0.0028996
A C 0.1036533
A A 0.0043957
C C 0.2016006
A A 0.0051138
A C 0.1065655
A C 0.1065747
A A 0.0031585
C C 0.2022020
C C 0.2095778
A C 0.1085457
C A 0.1066143
A A 0.0050391
C C 0.2065038
A C 0.1048536
A A 0.0082425
C A 0.1036056
C C 0.2012939
C A 0.1089108
C A 0.1041844
C A 0.1028691
A A 0.0054941
A C 0.1066732
C A 0.1062203
C C 0.2024171
C A 0.1082409
A A 0.0079531
C C 0.2075896
C C 0.2086618
C C 0.2009030
C C 0.2043583
A C 0.1027433
C A 0.1064741
C A 0.1084550
A C 0.1062956
C A 0.1087552
C A 0.1003688
A C 0.1076954
A A 0.0021614
C C 0.2058926
C C 0.2077966
A A 0.0088255
C C 0.2009546
C A 0.1033496
C C 0.2030929
C A 0.1094367
A A 0.0066950
C A 0.1097632
A A 0.0014252
C A 0.1026898
C C 0.2004895
A A 0.0025115
C A 0.1046488
A A 0.0028188
A C 0.1010309
C A 0.1001824
A A 0.0072118
A C 0.1070029
A A 0.0014907
C A 0.1092398
C C 0.2037578
C A 0.1079571
C C 0.2039170
A C 0.1078900
C C 0.2050323
A C 0.1007074
C A 0.1076159
A C 0.1039099
C A 0.1038567
A C 0.1028247
C A 0.1005284
C A 0.1084924
A A 0.0004356
C C 0.2057357
A A 0.0069600
A A 0.0094913
A A 0.0054146
C C 0.2030491
C C 0.2068785
A C 0.1012664
C C 0.2090525
C A 0.1034316
A A 0.0017198
A C 0.1009245
A C 0.1068556
C C 0.2017306
A C 0.1067565
C C 0.2014062
A A 0.0015376
A C 0.1047583
C A 0.1098352
C A 0.1079203
A C 0.1088965
C C 0.2084315
A C 0.1066086
C A 0.1090615
C C 0.2050194
C C 0.2067315
C C 0.2013299
A A 0.0091168
C A 0.1010853
A C 0.1045174
A A 0.0041893
A C 0.1043304
A C 0.1065061
C A 0.1075389
C C 0.2050606
A A 0.0081449
A C 0.1076916
A C 0.1053452
C A 0.1008132
A A 0.0038407
C A 0.1057814
C A 0.1080700
A C 0.1089578
C C 0.2062821
A A 0.0070441
C C 0.2093743
A C 0.1074053
C A 0.1070470
C C 0.2038438
C A 0.1095235
A A 0.0050486
C A 0.1045503
C C 0.2069982
A C 0.1057359
C A 0.1042752
A A 0.0089466
C A 0.1029824
C A 0.1031178
A A 0.0093870
C C 0.2040780
C A 0.1044772
A C 0.1099405
A C 0.1097643
C A 0.1076331
A A 0.0091503
A C 0.1092546
C A 0.1054719
C C 0.2073775
C A 0.1068021
C A 0.1007462
C A 0.1058175
A C 0.1097546
C A 0.1006635
C A 0.1086204
A C 0.1087185
A C 0.1049784
A C 0.1001977
A C 0.1015302
C C 0.2048015
A C 0.1072400
C C 0.2084621
C C 0.2087810
C A 0.1068725
C C 0.2090149
C A 0.1068327
C A 0.1044658
C C 0.2004135
A C 0.1075305
A C 0.1085318
A A 0.0059603
C C 0.2092286
A A 0.0040192
A C 0.1006736
A A 0.0084393
C C 0.2008492
A A 0.0064031
A C 0.1095494
A C 0.1077496
A C 0.1081119
C A 0.1017594
A C 0.1049967
A C 0.1053113
A C 0.1073927
C A 0.1006140
C C 0.2068344
A A 0.0008224
A C 0.1036102
A C 0.1030666
C A 0.1058666
C A 0.1012143
A A 0.0056010
A A 0.0011629
C A 0.1073621
C A 0.1093461
A A 0.0072568
A A 0.0070607
A A 0.0047138
A A 0.0053748
C A 0.1020702
C C 0.2041623
A A 0.0070479
C A 0.1073771
A C 0.1087822
C C 0.2050439
C C 0.2006254
A C 0.1097647
C A 0.1056063
A C 0.1082803
A A 0.0084556
C C 0.2058733
C A 0.1037796
A A 0.0020639
C C 0.2084784
C A 0.1099888
A C 0.1032313
A A 0.0089915
A A 0.0056860
C C 0.2023480
A C 0.1042078
A A 0.0094923
A A 0.0053080
C A 0.1051261
C A 0.1038632
A C 0.1057118
A C 0.1094236
A A 0.0094175
C A 0.1032157
C A 0.1012338
A A 0.0065028
A A 0.0035082
C C 0.2066001
A C 0.1025485
C A 0.1088288
C A 0.1016259
C A 0.1090762
C A 0.1053571
A A 0.0012706
C A 0.1047291
A C 0.1074995
C C 0.2078383
C A 0.1042556
A C 0.1050666
C A 0.1087901
C A 0.1001518
C C 0.2084834
A C 0.1076047
A A 0.0011402
A A 0.0040615
C C 0.2030513
C C 0.2001287
A C 0.1092634
A A 0.0038775
C A 0.1079434
A A 0.0093957
A C 0.1061099
C C 0.2086783
A C 0.1072238
A C 0.1057325
C A 0.1090037
A C 0.1062527
A C 0.1059294
C A 0.1050627
A A 0.0098811
C C 0.2052331
A C 0.1002454
A A 0.0088222
C A 0.1098436
C A 0.1084630
A C 0.1034789
C A 0.1088481
C C 0.2023805
A A 0.0089221

Associations on additive data

knitr::kable(assoc_qt(additive_data))
CHR SNP BP NMISS BETA SE R2 T P
1 snp_1 1 1000 0.1001 0.0001307 0.9983 766.1 0

Additive associations are detected awesomely!

Exclusive-or phenotype

Baron, Ronan, et al. “Elementary arithmetic operations by enzymes: A model for metabolic pathway based computing.” Angewandte Chemie International Edition 45.10 (2006): 1572-1576.

Exclusive-or phenotype

class: small-code

snvs <- create_snvs(
  n_snps = 2,
  n_individuals = 16
)
calc_xor_phenotype <- function(snvs) {
  if (ncol(snvs) < 4) {
    return(
      rep(3.14, nrow(snvs))
    )
  }
  0.1 * (snvs$snv_1a == snvs$snv_1b &
    snvs$snv_1a != snvs$snv_2a &
    snvs$snv_2a == snvs$snv_2b
  )
}
snvs$xor <- calc_xor_phenotype(snvs)
knitr::kable(snvs)
snv_1a snv_1b snv_2a snv_2b xor
A A A A 0.0
A A A C 0.0
A A C A 0.0
A A C C 0.1
A C A A 0.0
A C A C 0.0
A C C A 0.0
A C C C 0.0
C A A A 0.0
C A A C 0.0
C A C A 0.0
C A C C 0.0
C C A A 0.1
C C A C 0.0
C C C A 0.0
C C C C 0.0

Exclusive-or (XOR) trait

class: small-code

xor_trait <- create_custom_trait(
  phenotype = "xor",
  mafs = 0.49,
  n_snps = 2,
  calc_phenotype_function =
    calc_xor_phenotype
)
xor_data <- create_demo_assoc_qt_params(
  traits = xor_trait,
  n_individuals = n_individuals
)
knitr::kable(
  cbind(
    xor_data$ped_table[, -seq(1, 6)],
    xor_data$phe_table[, 3]
  )
)
snv_1a snv_1b snv_2a snv_2b xor
C A C A 0.0
C A C A 0.0
C A A A 0.0
C A A C 0.0
A A A C 0.0
C C C A 0.0
C A A A 0.0
A A A A 0.0
A C A A 0.0
C C C C 0.0
C C A C 0.0
C C C A 0.0
A C A C 0.0
C C A A 0.1
C C C A 0.0
C C A C 0.0
A C C A 0.0
C A A C 0.0
C C C A 0.0
A C A C 0.0
C C C A 0.0
C A C C 0.0
A C A A 0.0
C C C C 0.0
C C A A 0.1
A A A C 0.0
C C C C 0.0
A A A A 0.0
A C C C 0.0
A A A A 0.0
C C A C 0.0
A C C A 0.0
A C C C 0.0
C C C C 0.0
A A A C 0.0
C C A A 0.1
C A C A 0.0
A C C A 0.0
A A C A 0.0
A A C A 0.0
A C C A 0.0
A A A A 0.0
A A C A 0.0
C C A A 0.1
A C C A 0.0
C A A A 0.0
A A C A 0.0
C C C A 0.0
A C C C 0.0
A C A C 0.0
C A C C 0.0
C C A C 0.0
C A C C 0.0
A C A A 0.0
A C A A 0.0
A C C C 0.0
A A A C 0.0
A A A A 0.0
C C C A 0.0
A A C C 0.1
C A C C 0.0
C A C A 0.0
C A C C 0.0
A A A A 0.0
A C C C 0.0
C A A C 0.0
C C C A 0.0
A A A A 0.0
C A C A 0.0
C C C A 0.0
A C A A 0.0
A C A C 0.0
A A C C 0.1
C C A A 0.1
A A A C 0.0
C C A A 0.1
C A C C 0.0
A A A C 0.0
A C C C 0.0
C C A C 0.0
C C A C 0.0
A C C A 0.0
A A A A 0.0
A A A C 0.0
A A C A 0.0
C C C A 0.0
C C C C 0.0
A C A A 0.0
C A C C 0.0
C A A C 0.0
A C C C 0.0
A A A A 0.0
C C A A 0.1
A C A A 0.0
A C A A 0.0
A C C A 0.0
A C C C 0.0
A A A A 0.0
A A A C 0.0
A C C A 0.0
C A C C 0.0
A C C C 0.0
C A A A 0.0
A C A A 0.0
C A C C 0.0
C C A A 0.1
C C A A 0.1
C C A A 0.1
A C A A 0.0
A A A C 0.0
A A C A 0.0
A C C C 0.0
C C A C 0.0
C A A C 0.0
C A A C 0.0
C A A C 0.0
A C A A 0.0
C A C C 0.0
A A A C 0.0
A C A C 0.0
A C A A 0.0
C C A C 0.0
A A C A 0.0
A A A C 0.0
A C A C 0.0
A C C C 0.0
A A C A 0.0
A C C A 0.0
C C A A 0.1
C C A C 0.0
C C C A 0.0
A C A A 0.0
C A A C 0.0
C C C A 0.0
C C C C 0.0
C C C A 0.0
A C A A 0.0
C C C C 0.0
C A A C 0.0
C C A A 0.1
C A A C 0.0
C A A A 0.0
A C A A 0.0
A A C A 0.0
A C C C 0.0
A A A A 0.0
A A A C 0.0
C A C A 0.0
A C A A 0.0
A A C C 0.1
A A C A 0.0
C A C C 0.0
C C A A 0.1
A A C C 0.1
C C C A 0.0
A C A C 0.0
A A C C 0.1
C A C A 0.0
A C C C 0.0
A C C A 0.0
C C C C 0.0
C A A A 0.0
C A C C 0.0
C C C A 0.0
A C A A 0.0
A C A C 0.0
C A A C 0.0
A C C C 0.0
C C C C 0.0
C A C A 0.0
C C C C 0.0
C A A C 0.0
A C A A 0.0
A C A C 0.0
A A A A 0.0
A A A C 0.0
C A C A 0.0
A C A C 0.0
C A A C 0.0
A A A C 0.0
A A A C 0.0
A C A A 0.0
C C C C 0.0
A C A A 0.0
C C A A 0.1
C A A C 0.0
C A C A 0.0
C A C C 0.0
C C A A 0.1
A C A A 0.0
A A A C 0.0
A C A C 0.0
C C A A 0.1
C A A A 0.0
C A A A 0.0
C C C C 0.0
A A C A 0.0
C C A A 0.1
C A A A 0.0
A C C C 0.0
C A C C 0.0
A C C C 0.0
C C A C 0.0
A C A C 0.0
A C C C 0.0
A A C C 0.1
A C C C 0.0
C A C C 0.0
C A A A 0.0
A C A C 0.0
C A A A 0.0
C C C A 0.0
A C A A 0.0
A A C C 0.1
C C A A 0.1
A C A C 0.0
C C A A 0.1
C A A A 0.0
C C A C 0.0
C A C A 0.0
C A A A 0.0
A C C A 0.0
C A A C 0.0
C A C C 0.0
A A C C 0.1
A C A C 0.0
C A C A 0.0
A C C C 0.0
A C C C 0.0
C A A C 0.0
A A C C 0.1
C C C A 0.0
A A A A 0.0
C A C C 0.0
A C A C 0.0
A A C C 0.1
C A A C 0.0
C C C C 0.0
C A A C 0.0
C A C A 0.0
C C C A 0.0
C A A A 0.0
C C A C 0.0
C A A A 0.0
A A A C 0.0
C A A A 0.0
A C A C 0.0
C A A C 0.0
C C C A 0.0
A C A C 0.0
A A C C 0.1
A C C C 0.0
C C C C 0.0
C C A A 0.1
C C C A 0.0
C A A C 0.0
C A A A 0.0
C A C C 0.0
C A C C 0.0
C C C C 0.0
C A C A 0.0
C A C A 0.0
C C A C 0.0
A C A A 0.0
C A C C 0.0
C A C C 0.0
A A C C 0.1
C A C C 0.0
A C C A 0.0
C C C A 0.0
C C A A 0.1
A A C C 0.1
A C C C 0.0
C A C C 0.0
A C C A 0.0
A A A A 0.0
A A C C 0.1
C C A A 0.1
C C C A 0.0
A A A C 0.0
A A C A 0.0
C A A A 0.0
A A A C 0.0
A A C A 0.0
C C A A 0.1
C C C A 0.0
C C C C 0.0
C C A A 0.1
C C A A 0.1
C C C A 0.0
C C A A 0.1
A A A C 0.0
C C A A 0.1
C A C A 0.0
A C C A 0.0
A A A A 0.0
A C C C 0.0
C C C A 0.0
C A C C 0.0
A A A A 0.0
C A A C 0.0
C A C C 0.0
A C A C 0.0
C A C A 0.0
A C A C 0.0
A A C A 0.0
C A C C 0.0
C A A A 0.0
C C A A 0.1
A C A C 0.0
C A C A 0.0
A C A C 0.0
C A C C 0.0
C C C A 0.0
A A A C 0.0
C C C A 0.0
C A A C 0.0
A C A C 0.0
C A A A 0.0
C C A A 0.1
C C C A 0.0
A A C A 0.0
A A A C 0.0
C C A C 0.0
C C C C 0.0
C C C A 0.0
A A A C 0.0
A A A C 0.0
A A C A 0.0
C C C A 0.0
C A A C 0.0
C A A A 0.0
A A A A 0.0
C A A C 0.0
A C A A 0.0
A A C C 0.1
C C A C 0.0
C C A A 0.1
C A C C 0.0
A C A A 0.0
C A A C 0.0
C A A A 0.0
C A A A 0.0
C A A C 0.0
A A A A 0.0
A C A A 0.0
A A A C 0.0
C A C C 0.0
A A A A 0.0
A A A A 0.0
A C A A 0.0
C A A C 0.0
C C C A 0.0
A A A A 0.0
C C A C 0.0
A A C C 0.1
A A A A 0.0
C A A C 0.0
C A C A 0.0
A C C C 0.0
C A C C 0.0
A A C A 0.0
A C C A 0.0
A A A C 0.0
A A A C 0.0
C A C A 0.0
A A A A 0.0
C A A A 0.0
C C C A 0.0
A A C A 0.0
C A C C 0.0
C C A A 0.1
A C A A 0.0
C A A C 0.0
C C A A 0.1
A C A A 0.0
A C A A 0.0
C C C C 0.0
A C A C 0.0
A C C C 0.0
C A C C 0.0
A C C C 0.0
C A A A 0.0
A C C A 0.0
A C C A 0.0
C A C C 0.0
C C A A 0.1
A C A A 0.0
C C A C 0.0
A C A A 0.0
A A C A 0.0
A C C C 0.0
C A A C 0.0
C A A A 0.0
A A C A 0.0
A C A A 0.0
A A A A 0.0
A C C A 0.0
A A C A 0.0
A C C A 0.0
A A C A 0.0
A C C C 0.0
C A A A 0.0
A A A A 0.0
C A A A 0.0
C A A C 0.0
A C A A 0.0
A A C A 0.0
C A A A 0.0
C A A A 0.0
C C C A 0.0
A A C C 0.1
C A C A 0.0
C C A A 0.1
A C A A 0.0
C A A C 0.0
A C A A 0.0
A C A A 0.0
A C A A 0.0
C C A C 0.0
C A A C 0.0
A A C A 0.0
C A C C 0.0
A C A C 0.0
A A C C 0.1
C A A C 0.0
C C C A 0.0
A A A A 0.0
A C C A 0.0
C C A A 0.1
A C A C 0.0
A A C C 0.1
A A A C 0.0
C C A A 0.1
A A A A 0.0
C A C A 0.0
A A C A 0.0
A C C A 0.0
A C A A 0.0
C A C C 0.0
C A C A 0.0
A C A C 0.0
C A C C 0.0
C A A A 0.0
A C C C 0.0
C C A C 0.0
C A C A 0.0
C A A A 0.0
C C C A 0.0
C A C C 0.0
A C A A 0.0
A A C C 0.1
A A C A 0.0
A A A C 0.0
A C A C 0.0
C A C A 0.0
A A C C 0.1
A A C C 0.1
A A A C 0.0
A C A A 0.0
A A C A 0.0
A C C C 0.0
A A C A 0.0
A A A A 0.0
A A A C 0.0
C C C C 0.0
A A C A 0.0
A C A A 0.0
C C C A 0.0
A A C A 0.0
A A A A 0.0
C A C A 0.0
C A C C 0.0
C A C A 0.0
A C C A 0.0
A C C C 0.0
C C C C 0.0
A A A A 0.0
A A C C 0.1
A A C A 0.0
A A A C 0.0
C C A A 0.1
C A C A 0.0
C A C C 0.0
C A C A 0.0
C A C C 0.0
A A C C 0.1
C C C A 0.0
A A A C 0.0
C A C C 0.0
A C C C 0.0
A A A A 0.0
A A A A 0.0
A C C A 0.0
C A C C 0.0
A A C C 0.1
C C A A 0.1
C C C C 0.0
A C A C 0.0
A A C C 0.1
A A A A 0.0
C C C A 0.0
C C C A 0.0
C A A A 0.0
A A A C 0.0
C A C A 0.0
A C A C 0.0
A C A A 0.0
A A A C 0.0
A C C A 0.0
C C A C 0.0
A A A A 0.0
C C A C 0.0
C C A C 0.0
A C C A 0.0
A A A A 0.0
C C A C 0.0
C C A A 0.1
C C C A 0.0
C C A A 0.1
A A C C 0.1
C C C A 0.0
C C C C 0.0
C A A A 0.0
A C A C 0.0
C A A A 0.0
C C A C 0.0
C C C A 0.0
A A C A 0.0
C A A C 0.0
A A C C 0.1
A C C C 0.0
A A A C 0.0
A A C C 0.1
A C A A 0.0
C A C C 0.0
A A A C 0.0
A A C A 0.0
C C C A 0.0
A A C C 0.1
A A A A 0.0
C C A A 0.1
A A A C 0.0
A A C C 0.1
A C A C 0.0
A A A C 0.0
C A C A 0.0
C A A A 0.0
A A C C 0.1
A A C C 0.1
A C A A 0.0
A A C C 0.1
C A C A 0.0
A A A C 0.0
A C C A 0.0
A C A A 0.0
A A A C 0.0
A A C C 0.1
C A A A 0.0
A C C C 0.0
A C C A 0.0
A A C A 0.0
C A C A 0.0
A A C C 0.1
C C C C 0.0
C A C C 0.0
A C A C 0.0
C C A C 0.0
A C A A 0.0
C A C A 0.0
A A A A 0.0
C C C C 0.0
A C A A 0.0
A A C C 0.1
C C C A 0.0
A A C A 0.0
A C C C 0.0
A C C C 0.0
A C A A 0.0
A A A C 0.0
A C A A 0.0
C A C A 0.0
A C C C 0.0
A C C C 0.0
C C A C 0.0
C A C C 0.0
A A A A 0.0
A A A A 0.0
A C A A 0.0
A C C C 0.0
C A A C 0.0
C C C A 0.0
C C C A 0.0
C C A C 0.0
A A C C 0.1
C A C C 0.0
C C A A 0.1
A C C C 0.0
A A C A 0.0
C A C C 0.0
C C A C 0.0
A A A C 0.0
A A A C 0.0
C A C C 0.0
A C A A 0.0
A A A A 0.0
C C A A 0.1
A A A C 0.0
A C A A 0.0
A A C C 0.1
A A C C 0.1
C C C A 0.0
A C A C 0.0
A A A A 0.0
C C C A 0.0
A A C C 0.1
C A A C 0.0
C C C C 0.0
A C A A 0.0
C A A C 0.0
C A C C 0.0
A A A A 0.0
C A A C 0.0
C C A A 0.1
C C C A 0.0
A C A A 0.0
C A C A 0.0
A A C A 0.0
A C A A 0.0
C C A C 0.0
A A C C 0.1
A A A C 0.0
A A A A 0.0
A A C A 0.0
A C A A 0.0
C A A C 0.0
A C A C 0.0
C A A C 0.0
A C C C 0.0
A C C C 0.0
A C C C 0.0
A C C C 0.0
C A A A 0.0
A A C A 0.0
A C C A 0.0
C A C C 0.0
C C C A 0.0
C A A C 0.0
C A C C 0.0
C A C A 0.0
C A A A 0.0
A A A A 0.0
C C C A 0.0
C C C C 0.0
C A C C 0.0
C A C A 0.0
A A C A 0.0
C A A C 0.0
C C C A 0.0
C C A A 0.1
A C C A 0.0
A A C A 0.0
A C C A 0.0
A A C C 0.1
C A C C 0.0
A C A C 0.0
A A C A 0.0
C A A A 0.0
C C A A 0.1
A A A C 0.0
A C C C 0.0
C A A A 0.0
C C C C 0.0
A C A A 0.0
C C C A 0.0
C A A A 0.0
C A A C 0.0
A C C A 0.0
A A C C 0.1
A A C C 0.1
C C A C 0.0
C A C A 0.0
C C C C 0.0
A C A C 0.0
A A C A 0.0
C C A C 0.0
C C A A 0.1
C A C A 0.0
A C A C 0.0
C A A A 0.0
A C A C 0.0
C A A A 0.0
C A A C 0.0
C C C A 0.0
A C C C 0.0
C C A C 0.0
C A C C 0.0
C C A A 0.1
A A A A 0.0
A A A A 0.0
A C C C 0.0
C C A C 0.0
C C A A 0.1
C C C C 0.0
A C C A 0.0
C C C A 0.0
C A A A 0.0
C C C A 0.0
A A C C 0.1
C C C C 0.0
A C A A 0.0
A C A A 0.0
C A C A 0.0
A C C A 0.0
C C A C 0.0
C C C C 0.0
A C C A 0.0
A C A A 0.0
C C C C 0.0
C C A C 0.0
C C A C 0.0
A C A A 0.0
A A A C 0.0
A A A C 0.0
A C C A 0.0
C C C C 0.0
C C A A 0.1
C A C A 0.0
C C C C 0.0
C A C A 0.0
A A A C 0.0
C A C C 0.0
C A C A 0.0
A C A C 0.0
A A C C 0.1
A C A A 0.0
A A A A 0.0
A A A C 0.0
A A C C 0.1
A A C C 0.1
A A C C 0.1
C C C C 0.0
A A C A 0.0
A C A A 0.0
A A A A 0.0
A C A C 0.0
A A C A 0.0
C C A C 0.0
A A A A 0.0
A A A C 0.0
A C A A 0.0
C C A A 0.1
C A A A 0.0
A C A A 0.0
A A A A 0.0
C A A A 0.0
C A A A 0.0
A A C C 0.1
A C C C 0.0
C A A A 0.0
C A C A 0.0
A A A A 0.0
C C C A 0.0
C C A C 0.0
A C A C 0.0
A A C C 0.1
C A C A 0.0
C A C C 0.0
A C A A 0.0
A A A C 0.0
C A A A 0.0
C A A C 0.0
C A A C 0.0
A C A C 0.0
C A A C 0.0
A C A A 0.0
A C C A 0.0
C A A C 0.0
C C C A 0.0
C A A C 0.0
C C A A 0.1
C A C A 0.0
C C A A 0.1
C C C A 0.0
C A A A 0.0
C C C C 0.0
A C C C 0.0
A A C C 0.1
C C A A 0.1
C A C A 0.0
A A A C 0.0
A A C A 0.0
A C A A 0.0
A C C C 0.0
A A C A 0.0
C A A A 0.0
A A A C 0.0
A C C C 0.0
C A A A 0.0
C A C C 0.0
C A C A 0.0
A C C A 0.0
C A C A 0.0
C C C A 0.0
C A C A 0.0
A A A C 0.0
C C C C 0.0
A C A C 0.0
C C C C 0.0
A C C A 0.0
A C A C 0.0
A A C A 0.0
C C C C 0.0
C A A C 0.0
A C A C 0.0
A C A C 0.0
C A A C 0.0
C A C C 0.0
A A A A 0.0
A A A A 0.0
C C A C 0.0
C A C A 0.0
C C A A 0.1
A A A C 0.0
A C A A 0.0
A C C A 0.0
A C C A 0.0
C A C C 0.0
A A C C 0.1
A A C A 0.0
A C A C 0.0
A C C C 0.0
C C C C 0.0
A C A C 0.0
A A C C 0.1
A A A C 0.0
A C C C 0.0
A A C A 0.0
A C A A 0.0
A C C C 0.0
C C C C 0.0
C C C C 0.0
C A A C 0.0
A C C C 0.0
C A C A 0.0
C A C C 0.0
A C A A 0.0
A C C C 0.0
A C C A 0.0
C C A A 0.1
A C A C 0.0
C A A C 0.0
A A C A 0.0
A C C C 0.0
A C C C 0.0
A C A C 0.0
C A A C 0.0
A A C C 0.1
C C C A 0.0
C C C A 0.0
A C A C 0.0
C A C A 0.0
C C C C 0.0
C A C A 0.0
A A A A 0.0
C A A A 0.0
A C A A 0.0
A C A C 0.0
A C A C 0.0
C C A C 0.0
C A C A 0.0
A C C C 0.0
C A C A 0.0
C C C C 0.0
C A A A 0.0
A A C C 0.1
A C C C 0.0
A A C A 0.0
A C A C 0.0
C A A A 0.0
C A A A 0.0
A A A C 0.0
C A C A 0.0
C C A C 0.0
C A A C 0.0
C C C C 0.0
A A C C 0.1
C A C A 0.0
A A C A 0.0
A A C C 0.1
C A A A 0.0
C C A A 0.1
C A A C 0.0
C C A A 0.1
C C C C 0.0
A C A A 0.0
C A C A 0.0
A A A A 0.0
C C C C 0.0
A C A C 0.0
A A C A 0.0
A C A A 0.0
C A A A 0.0
C A A C 0.0
A A A A 0.0
C C A C 0.0
C C C C 0.0
C C C C 0.0
C A C A 0.0
A A A A 0.0
A A A C 0.0
A C C C 0.0
C A A C 0.0
A C C C 0.0
C A C C 0.0
A C C A 0.0
A A C A 0.0
C A A C 0.0
C A A A 0.0
C C A C 0.0
C A A C 0.0
A C A A 0.0
A A C C 0.1
C A C C 0.0
A A A A 0.0
A C C C 0.0
C A C C 0.0
C C A A 0.1
C A C C 0.0
C A A A 0.0
C C A A 0.1
A C A C 0.0
A C C C 0.0
C A C C 0.0
C C C C 0.0
A C C C 0.0
A C A C 0.0
A C A A 0.0
C A A C 0.0
C A C A 0.0
C C C A 0.0
A C A C 0.0
A A C A 0.0
A C C A 0.0
A C C C 0.0
A C C C 0.0
C A A C 0.0
A A C A 0.0
C C A C 0.0
A C A C 0.0
A C A A 0.0
A A A C 0.0
C A A A 0.0
C A C A 0.0
A C C C 0.0
C C A C 0.0
A C C A 0.0
C C C A 0.0
C C A A 0.1
A C A A 0.0
A C C A 0.0
A A A A 0.0
A C C C 0.0
C A C A 0.0
A A A A 0.0
A C C C 0.0
A C A A 0.0
C C A C 0.0
A A C A 0.0
C C A C 0.0
C A A A 0.0
C A A A 0.0
C A A C 0.0
C C C A 0.0
C C A C 0.0
C C A A 0.1
A A A C 0.0
A A A C 0.0
C A A A 0.0
C C A A 0.1
A A C C 0.1
A A A A 0.0
A A C C 0.1
A C C A 0.0
C C A C 0.0
A A C A 0.0
C A C C 0.0
A C C A 0.0
A A A A 0.0
A C A C 0.0
A C C A 0.0
A A C C 0.1
C A C C 0.0
A A A A 0.0
A C C C 0.0
C A A C 0.0
C A C C 0.0
A C A A 0.0
A C C A 0.0
C C C A 0.0

Associations on exclusive-or (XOR) data

knitr::kable(assoc_qt(xor_data))
CHR SNP BP NMISS BETA SE R2 T P
1 snp_1 1 1000 0.0005299 0.001523 0.0001212 0.3479 0.7280
2 snp_2 2 1000 0.0004813 0.001452 0.0001101 0.3315 0.7403

ML can do exclusive-or (XOR)

Exponential phenotype

Exponential

Exponential phenotype

class: small-code

snvs <- create_snvs(
  n_snps = 3,
  n_individuals = 16
)
calc_exp_phenotype <- function(snvs) {
  as <- seq(1, ncol(snvs), by = 2)
  bs <- as + 1
  h <- snvs[, as] == snvs[, bs] & snvs[, as] == "C"
  10 ^ rowSums(h)
}
snvs$exp <- calc_exp_phenotype(snvs)
knitr::kable(snvs)
snv_1a snv_1b snv_2a snv_2b snv_3a snv_3b exp
A A A A A A 1
A A A A A C 1
A A A A C A 1
A A A A C C 10
A A A C A A 1
A A A C A C 1
A A A C C A 1
A A A C C C 10
A A C A A A 1
A A C A A C 1
A A C A C A 1
A A C A C C 10
A A C C A A 10
A A C C A C 10
A A C C C A 10
A A C C C C 100

Exponential trait

class: small-code

exp_trait <- create_custom_trait(
  phenotype = "exp",
  mafs = 0.49,
  n_snps = 8,
  calc_phenotype_function =
    calc_exp_phenotype
)
exp_data <- create_demo_assoc_qt_params(
  traits = exp_trait,
  n_individuals = n_individuals
)
knitr::kable(
  cbind(
    exp_data$ped_table[, -seq(1, 18)],
    exp_data$phe_table[, 3]
  )
)
snv_4a snv_4b snv_5a snv_5b snv_6a snv_6b snv_7a snv_7b snv_8a snv_8b exp
C C A C A A A C A C 1e+01
A A A C A A C A C A 1e+00
C C A A A C C A C A 1e+02
A C A C C C A C C C 1e+03
A C C A A A A C C C 1e+02
C C C A C C C A A A 1e+02
C A C C A A A A A C 1e+01
A A C C C A C A C A 1e+01
C A C C A C A A A C 1e+02
A C C C A C A C A A 1e+03
A A A C C C C C A A 1e+04
A C C A A A A C A C 1e+00
A A C C A C A A C A 1e+01
C C C C C C A A C C 1e+04
A A A A A C C C C A 1e+01
A C C A A C A C C C 1e+02
C A C A C C A C C A 1e+01
A A C C A C C A A A 1e+01
A A A C A A C A A C 1e+00
A A A C C A C A A C 1e+01
C A A C C C C C C C 1e+04
A A C C C A C A C C 1e+02
C C A C C A A C C C 1e+03
A C A A C C C A A A 1e+02
C A C A C A A A A A 1e+00
A A C C C A C A A C 1e+02
A A A A C C C C A A 1e+03
C A A C A A C A A A 1e+01
C C A A C C C A C A 1e+02
A A C A C A A C A C 1e+00
C A A A A A C A A A 1e+00
A C A A A A C C C A 1e+01
A C A C C C A A A A 1e+01
A A C C A A C A C A 1e+01
A A A C C C C C C C 1e+03
C C A A C C C C A C 1e+04
C A C A C C A A C A 1e+02
C A C C A A C C A C 1e+03
A A C C C C C C C A 1e+04
C C C A C A A A A A 1e+02
A C C C C A A A A A 1e+01
A A C A A A C C A C 1e+01
C C C A A A A C C C 1e+04
A C C C C C A A A C 1e+04
A C A C A C C C A C 1e+01
A C A A A A A A A A 1e+01
A C C A C A A A A A 1e+01
C C A A A A C A A A 1e+01
A C C A A A A C A C 1e+01
A C A C C C C A C A 1e+02
C A A C C A A C A A 1e+01
C A C A A C C C C C 1e+02
C A A C A C C C C A 1e+01
A C C C C A A A C C 1e+02
A C C A C A C A A A 1e+02
C C C C A A A C C C 1e+04
C C A C A A A A A C 1e+01
A A A A A A C C A A 1e+01
C A C C A C A A A A 1e+03
C A C C C C C A C C 1e+04
C C C A C C C C A C 1e+04
C C A C C A A C A A 1e+02
A C A A C A C C A A 1e+03
A A C A C A C C A A 1e+02
C C C C A A C C A C 1e+04
C A C A C C A C A A 1e+01
C C C A A C C A A A 1e+01
A C C C C A C A C A 1e+01
A C A C A C A C C A 1e+01
A A C C C C C C A A 1e+03
A C C A C A A C A A 1e+01
C A A A A C A A C A 1e+01
A A C A C C A C A A 1e+02
A A C C A A C C A C 1e+02
C C A C C A A C C A 1e+02
C C C C A C C A A A 1e+03
C C A A A A A A A A 1e+02
C C C A C C C C C A 1e+03
C C A C A C A A C C 1e+02
A A A A A A A A C C 1e+01
A C C A A C A A C C 1e+02
A C C C A A A C A C 1e+03
A C A C A A C C A A 1e+02
C A C A A A C C C A 1e+01
C C A A A C A A A C 1e+01
C A A A C C C C C C 1e+04
C A A C C A C C A A 1e+02
C A A C A A C C A A 1e+02
C C C A A C C C A A 1e+02
C C A C A C A A C A 1e+01
A A C A C A C C A C 1e+01
C C A A C A C A A A 1e+01
A C C C A C A A C A 1e+01
C C A A C C A A C A 1e+03
C A C C A A C A A A 1e+01
A C A C C A A A A A 1e+00
A C A C A A C A A C 1e+00
A C C C C C A C C C 1e+03
C C C A A C A A C C 1e+03
A A C C C A C A C A 1e+01
C C C C A A C C C A 1e+04
A A C C C A C A A C 1e+02
C C A C C C C A A A 1e+04
C C C A A C A A C C 1e+03
C C C C C A C C C C 1e+04
A A A A A A C A C C 1e+01
A C C A C A C C C C 1e+05
C C A A C A A A A A 1e+01
A A A A A C A C A A 1e+03
A C C A A A C C C C 1e+03
C A A C A C C A C C 1e+01
A C C A C C A C A A 1e+02
A A A C C A A C C A 1e+00
C A A A A A C C A C 1e+02
C A C A C A C A A A 1e+00
C A C C C C C A A C 1e+04
C C A A C A A C A C 1e+03
A A C A A A C A A A 1e+00
A A A C A A A C A A 1e+00
C A C C A C C A C A 1e+01
A A A C C C A C C A 1e+01
A C A C A C C A A A 1e+00
A A A C A A A C C A 1e+00
C A A A A A C C A A 1e+03
C A C A C C A A C A 1e+01
C C C A A A C C C C 1e+03
C C C C C C C A C A 1e+03
A C C C C A A C C C 1e+04
C C A A A C A C A A 1e+02
A C A C C A A C A C 1e+01
C C A C A C A C A A 1e+01
C C A A C C A C A A 1e+02
C C A A A C A A A C 1e+01
C C C A A C C A C A 1e+03
A C A A A A C A A A 1e+01
A C A A C A C A C A 1e+00
C C C A A C C A A A 1e+02
A C A C A C A A A A 1e+01
C A C A C C A C A A 1e+02
C A C C C A A C A A 1e+01
A A A A A A C C A C 1e+03
C C A A C C C A A C 1e+03
C A C A A C C C A C 1e+02
A A C A C A A C A C 1e+01
A A C A C A C C A C 1e+01
A A A A A A A C C A 1e+02
A C C A C C C C A A 1e+03
A A A A C C A C A C 1e+02
C A C A C C C A C A 1e+01
C C C C A A A A C A 1e+02
A A A C A A A A C C 1e+01
C A A A C C C C C C 1e+04
C A A A C C C A C A 1e+01
C A A A C A C A C C 1e+01
A C C A C C C A A A 1e+02
A A A C A A C C A C 1e+03
A A C C A C C A C A 1e+03
A C C A A A A A A C 1e+02
C C C C C A A A C A 1e+03
A C A A C A A C C C 1e+02
C C A A A C C A C C 1e+02
C A A C C A A A C A 1e+02
A C A C A A C A C A 1e+00
A C C C C C C A C C 1e+06
A C A C C C C A C A 1e+03
C C C C C C A A C C 1e+05
C A A C A C A C C A 1e+00
C C A C A A C A C A 1e+02
A A C A A C A C C A 1e+00
A C C A C C A C C A 1e+03
A A A A C C C A C C 1e+04
A A C C A A C A C A 1e+01
C A A C A A C A C C 1e+02
C A C A C A C C C A 1e+01
C C A C A C C C A C 1e+03
C A A A A A C A A C 1e+01
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C C A A A A A C A A 1e+02
C A C C A C C A C A 1e+03
C C A A A A C C A C 1e+02
C A C A A A C C A A 1e+02
A A C A A A A C A A 1e+00
A A C A C A C A A A 1e+01
A C A C A C A A A C 1e+01
A C C A C C C C A C 1e+03
C C A C A A C C C C 1e+03
C C A A A A C C A C 1e+04
A A C A A C A A A A 1e+01
A C C C C A C A A C 1e+02
C C A A A A A C C C 1e+04
A C C A C A A C A C 1e+01
A C A A C C A C C A 1e+03
C A C C A C A A C C 1e+03
C A C C C A A C A C 1e+02
A A C C A A C C A A 1e+02
C C A A A C A C C A 1e+01
C A C A A A C A C C 1e+02
A A A A C C A C A C 1e+02
A C A C A A C A A A 1e+00
A C C A C A A A A C 1e+01
C A C A A A A C C A 1e+03
A C C C C C C A A C 1e+02
C C A C A C C C A C 1e+02
C C C C C A C A C C 1e+04
C C C C A A C A A A 1e+04
C C C A C A C A A A 1e+02
A C A A C A A A A C 1e+00
C A A C C C C C A A 1e+04
A A A C C C A A C C 1e+03
C A C A C A A A A C 1e+01
A C A C A A C A A A 1e+01
A C A A C C C A C C 1e+02
C A C C C A A A C A 1e+01
C C A C A A A C C A 1e+03
A A A C A A A C C A 1e+02
A C A A C C A A C A 1e+01
A C C A A C C A C C 1e+02
A C C A C C C A A C 1e+03
A C C A A C C A A A 1e+00
C C A A A A C C A C 1e+03
A A C C A A C A A C 1e+03
C A A A A C C A A C 1e+01
A A A A A A A C A C 1e+00
A A C C A C A A C C 1e+03
A A C C C C A C C A 1e+03
C C A C C A C C C C 1e+04
C C C C C C A A C C 1e+05
A A A A C A C C C C 1e+02
A A C C C A C A C C 1e+02
A C A C C C A A C A 1e+03
A A A C C C A C A C 1e+02
A A C A A A A C C C 1e+01
A A A A C C C C C A 1e+03
A C A A A C A C A C 1e+00
A A C C C A A A A C 1e+03
C A C C C C C A C A 1e+03
A C A A C C A C C C 1e+03
A A C C C C C A A C 1e+03
A A C C A C C C C C 1e+04
C A C A C C A C C C 1e+03
A C A C A C A C C A 1e+01
A A A C A C A C A A 1e+01
C C A A A C A C A C 1e+02
C A A A A C A C C A 1e+01
A C A C A A A A A C 1e+00
A C C C A C C C C C 1e+03
C A A C A A C C C C 1e+02
A C C A C C A C C C 1e+03
A A A A C C C A C C 1e+03
A A A A A A C A C A 1e+01
C C C A A A A C A A 1e+01
A A C A C C C C A A 1e+03
C A A A A C A A A C 1e+01
A A C A C C C C A A 1e+02
A A A A C A C C A A 1e+01
C A A A C A A A C C 1e+01
A C C C C C C A A A 1e+04
A A A A C C A A C C 1e+03
C C C C C A A C C C 1e+03
C A C C A A A A A C 1e+01
A C C C A A C C A A 1e+02
A A A A C C A C C C 1e+02
A C A A A A A A C A 1e+00
C A A A A A C A A C 1e+00
A C C A C C A A A A 1e+01
A C C C A A A C A C 1e+01
A C C A A C A A A C 1e+00
C C A A C C C A A C 1e+04
A C A A A A A C C C 1e+02
C A A A C A A C C C 1e+02
A A C A C A C C A A 1e+02
A A C A A C A C A A 1e+02
C A A A A A C A A C 1e+00
A A A C A C A A A C 1e+01
C C A C A C A A A A 1e+03
A A C A C A C A A C 1e+01
C C C A A A C A C C 1e+03
A A A C A A A C A C 1e+01
C A A C C A C A A C 1e+02
A C A C A A C C C A 1e+03
C A C C C C A C C A 1e+03
A A A C A A C C C C 1e+02
A C C A A A C A C A 1e+00
C A C A C A C A A A 1e+01
A C A A A A A C C C 1e+02
A A C A C A A A C C 1e+02
A C C A A A C A A C 1e+03
A C C A C A A C A C 1e+00
A C C C A A A C A A 1e+01
C C C C A C C A A A 1e+03
C A A A A A C C A C 1e+01
C A A A C A C C A A 1e+04
C A C A C C A C C A 1e+01
A A C C C C C A A C 1e+03
C C C C A A C A C A 1e+03
A C C C A C A C C A 1e+01
A C A C A A A C C C 1e+03
C A A C A C A A A C 1e+01
C C C A C C A C A C 1e+04
C A C C C C A C A A 1e+03
C A A C A C A C C A 1e+01
A C C C C C A C C A 1e+03
C A C A A A A C C A 1e+00
A C C A A A C C A A 1e+03
A A A A C C C A A A 1e+01
A A C A C C A C A A 1e+02
A C A A C C C A C A 1e+03
A C A A A A A A C A 1e+02
A A C A A C A C C C 1e+01
A C C A C C A C A C 1e+01
C A C C C C A A A A 1e+02
C A C A C A C C C C 1e+02
A A C A C A A A C C 1e+01
C A C C A A A A C A 1e+02
C A C C C A C A C C 1e+02
A C A A C A A C C A 1e+01
A A C A A C A C A A 1e+00
A C A A A A C C A C 1e+01
A A A A A C C C C A 1e+01
A C C C A A A A A C 1e+02
A A C C C A C A C A 1e+01
A A C A A C A A A A 1e+01
A A C C C A A C C A 1e+02
A A A A C C C A C A 1e+02
C C A C C A C A A A 1e+02
A C C A A A C A A A 1e+00
A A C C A A A A C A 1e+02
A C A A C A A A C A 1e+00
C C C C A A A C C A 1e+02
A A A A A C C A A C 1e+01
C A A A C A C A C A 1e+00
C A A A A A C C A C 1e+01
A A C C C C A A A A 1e+03
C A A A C C C A A A 1e+02
A A A A C C C C A A 1e+03
C C A C A C C C C A 1e+03
A A C C C A A C C C 1e+03
A A C C C A A A C C 1e+04
A C C C A A A A A A 1e+03
A A C C C C A C C C 1e+04
A C C A C A C C A A 1e+02
A C A A C C C C C C 1e+04
A A C A A A C A A C 1e+01
A A C C C C C C A C 1e+04
C C A C A A A A A C 1e+02
A A A A C C A C C C 1e+03
A A C C C A A A C C 1e+02
C C C C C A C A C A 1e+02
C C C C A A A A C A 1e+02
C A C C A A A C C C 1e+02
C C A A A A C C C C 1e+04
C C A C C C C A A C 1e+04
C A A C C C C A C A 1e+02
A A A A A C A C C C 1e+03
C A C C A A C A C C 1e+02
A C A A C C A C C A 1e+01
C C A A A A A C A A 1e+02
C A A A A A A A A C 1e+01
C A C A A C C A C C 1e+01
C A A A A C A A C A 1e+01
C C A A C A C C A C 1e+03
A A A A A A C C C C 1e+03
A A C C C C C A A C 1e+03
C C C C A A A A C C 1e+03
A C A C C A C A A C 1e+01
A C A C A C C C C C 1e+03
C A A C A C A A A A 1e+00
C A C C C A C A A A 1e+02
A C C A C A A A A C 1e+01
A C A A A C A C A A 1e+00
C C A C A C C A C C 1e+03
A A C C C A A A C C 1e+02
C A A A C A A A C A 1e+00
A C A C A A A A A C 1e+01
A A A A A C A A A C 1e+01
A A C C A C C C C A 1e+03
C A A A C A A A C C 1e+01
C A A A A A C A A A 1e+00
C C C A C C C C A C 1e+04
A A C A A C A C A C 1e+01
A A A A C C A C A C 1e+02
A C A A A A C C A A 1e+01
C A C C C A A A C C 1e+02
A C C A C A A A A A 1e+00
A A C A C C A C C A 1e+02
C C C A C A C A A C 1e+01
A C C A A C A A C C 1e+03
A C C C A A A C C C 1e+04
C C C A A A C A A C 1e+01
A A A A C C A C A A 1e+01
A A C C C C A C A C 1e+03
C C C A A A C A A C 1e+02
C A A C A A A A A A 1e+01
C C A A A A A C C C 1e+03
A A A C C A C A C A 1e+00
C A C A C A C A A C 1e+00
C C A C A A A C A C 1e+01
C C C C C C A C A A 1e+03
A C C C A C C A C A 1e+04
C C A C C C A A A A 1e+03
C A A A A A C C C A 1e+01
A A C C A A C A A C 1e+03
A A C A A A A C A A 1e+02
A C C C A A C C C A 1e+03
A A C C C A C C A A 1e+02
C A A A A C C C C A 1e+01
C C C C C A A C A C 1e+03
C A A A C C C C C C 1e+04
C C A C C A A C A A 1e+02
A C C C A A C C C C 1e+03
C C C C C A C C A C 1e+04
A C A A A C C A C A 1e+01
C A A A C A A C C C 1e+02
A A A C A A A A A A 1e+00
A A A A C C C A C A 1e+02
C A A A A A A A C C 1e+02
A C A A A C A A C C 1e+02
A A A A A A A A A A 1e+00
A A A A A A C A A A 1e+01
C C C A C C C A C A 1e+02
C A A C C C C A C A 1e+01
C A C A A A C A C A 1e+01
C A C C C A A C A A 1e+01
C C C A C C A A C A 1e+03
A A C C C A C C C A 1e+03
C A C C A C A A C C 1e+02
A A C A A A C A A C 1e+01
A A C C C A A A C C 1e+03
C A C C C A A C C C 1e+02
C A A C C C C C A C 1e+02
A A C C A A A A A A 1e+02
A A A C A C C C A C 1e+03
C A C C C C C C C C 1e+04
C A C A C C A A A A 1e+01
C C A C A C C A A C 1e+02
C C C C A A C A A C 1e+03
A C A C C A C A C C 1e+01
A A C A A C C C C C 1e+02
A A A A C C C C A C 1e+04
A C A C A C A A A C 1e+00
C C C C A A C A C A 1e+03
A C A A A A A A C A 1e+01
A A C A C A A A C A 1e+00
C A C A C A A A C C 1e+01
A A A A A A A C A A 1e+01
A A C C A A A A A A 1e+01
C A C C C A A A A A 1e+02
A C C A A C A C C A 1e+01
A C C A A C C A C A 1e+00
C A C A C A C C A A 1e+01
A A C A A C C A C A 1e+01
A C A C A A C A C A 1e+00
A A C A A C A A C A 1e+00
C C A A C C A C C A 1e+02
A C C C C A C A A C 1e+02
A A C A A C C A A C 1e+01
A A C C C C A A C C 1e+03
A A C A A A A A A C 1e+00
A A C A C A A A C C 1e+02
A C A C A A A C A C 1e+01
A A A A C C C A A A 1e+02
A C C C A C A C C A 1e+03
C C A A C A A A A A 1e+02
C A C A A A C C A C 1e+03
A C C C A A A A A A 1e+02
C C A A C A A C C A 1e+01
A C C A C C C A A A 1e+01
A A A C A A C A C A 1e+00
C C A A A A C A C C 1e+03
C C A C C A C A A A 1e+02
A A A A A A A A A A 1e+00
A A C A A A A C C A 1e+01
A C A A A C C A A A 1e+00
C C A C C C A A C C 1e+04
A A A C A C C C A A 1e+01
C C C A C C C C A C 1e+04
A A C C C C C A C A 1e+03
A A C C C C A C C A 1e+03
A C A C C C C C C C 1e+03
C C C C A A A A C C 1e+05
A A C A A C C C A A 1e+01
C C C C C C A A C A 1e+03
A A C A C A A A A A 1e+02
C A A C C A C C C C 1e+05
C A A C A A A A C C 1e+01
C A A A C C C A A A 1e+01
A C C A A C C C A A 1e+03
C C A C A A C C C A 1e+03
C A A A A A C A C A 1e+00
A A C C C A A C C C 1e+03
A A A C A C A C C A 1e+00
C C A C A C A A A A 1e+03
A A C A A C A A A A 1e+01
A A C A C C C C A C 1e+02

Associations on exp data

knitr::kable(assoc_qt(exp_data))
CHR SNP BP NMISS BETA SE R2 T P
1 snp_1 1 1000 8780 2889 0.0091700 3.0390 0.0024340
2 snp_2 2 1000 4418 2881 0.0023510 1.5330 0.1255000
3 snp_3 3 1000 8600 2866 0.0089410 3.0010 0.0027610
4 snp_4 4 1000 7132 2836 0.0062980 2.5150 0.0120600
5 snp_5 5 1000 2470 2861 0.0007464 0.8634 0.3881000
6 snp_6 6 1000 10940 2802 0.0150400 3.9040 0.0001011
7 snp_7 7 1000 9149 2882 0.0099980 3.1750 0.0015460
8 snp_8 8 1000 10860 2888 0.0139800 3.7620 0.0001785

Features of examples

Enroth et al. “Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs.” Nature communications 5.1 (2014): 1-11.

Your example

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Conclusion

Questions

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Publishing strategy

Publication model Classical Registered report
Significant results Can publish Can publish
No significant results Cannot publish Can publish

Publication pressure was associated with higher odds of engaging frequently in ≥1 QRP (OR 1.22, 95% CI: 1.14, 1.30)